The present invention is directed to methods of identifying target nucleic acid sequences which are predictive of disease states or biological conditions in cells containing the nucleic acid sequence.
Recent advances in genomics, molecular biology, and structural biology have highlighted how RNA molecules participate in or control many of the events required to express proteins in cells. Rather than function as simple intermediaries, RNA molecules actively regulate their own transcription from DNA, splice and edit mRNA molecules and tRNA molecules, synthesize peptide bonds in the ribosome, catalyze the migration of nascent proteins to the cell membrane, and provide fine control over the rate of translation of messages. RNA molecules can adopt a variety of unique structural motifs, which provide the framework required to perform these functions.
The many functions of RNA molecules has also solidified their importance as therapeutic drug and diagnostic targets. Indeed, many investigators are pursuing mRNA transcripts and proteins produced therefrom that are expressed at different levels in cancer vs. normal cells in order to develop therapeutic and/or diagnostic compounds which modulate the cancer-causing mRNA transcript or protein. Indeed, 500 transcripts have been reported to be expressed at significantly different levels (15-fold on average) in normal vs. gastrointestinal tumor cells. Zhang, et al., Science, 1997, 276, 1268-72. Many genes have as many as 10-20 alternative transcript forms that, in some cases, have been associated with a cancer phenotype. For example in cancerous cells, transcription of the mdm2 gene is initiated at a distinct site not used in normal cells. Landers, et al., Cancer Res., 1997, 57, 3562-3568, incorporated herein by reference in its entirety. In the Bcl-x mRNA, alternatively spliced forms of the transcript result in dramatically different cell behavior and sensitivity to chemotherapeutic drugs. Kuhl, et al., Br. J. Cancer, 1997, 75, 268-274, which is incorporated herein by reference in its entirety.
A universal technology platform to attack multiple forms of cancer has widely been believed to be impossible due to the heterogeneous nature of cancer. Thus, traditional cancer therapeutics has focused on individual cancer pathways and modulation of individual proteins and/or mRNA transcripts associated with the suspected causative pathway of the disease state. An unconventional, broadly applicable approach to cancer diagnosis and treatment, however is greatly desired. Accordingly, the present invention provides the means to identify distinguishing features of types of cancer coupled with a common molecular mechanism to diagnose and selectively destroy the cancer cells or other cells associated with a disease state or biological condition. It is a principal object of the invention to identify a target nucleic acid sequence which is predictive of a disease state or biological condition in cells containing the nucleic acid sequence.
The present invention is directed to methods of identifying target nucleic acid sequences which are predictive of preselected disease states or biological conditions in cells containing the nucleic acid sequence. Members of a set of mRNA molecules from a common gene, but containing different sequences and structures, are compared. The gene is predictive of the disease state or biological condition in cells containing the gene. At least one molecular interaction site from among those present in the members of the set are identified. The molecular interaction site is present in cells likely to have the disease state or biological condition. At least one nucleic acid sequence from the molecular interaction site is ascertained.